Hi,

This is a fairly basic question about syntax. How does one: as surface the protein and pseudoatoms in the short script below? Moreover, and work with the Lysine amines rather than the alpha carbons?

# for_gnp.py

# fetch a protein and create whole phage
cmd.fetch("1ifp", type="pdb1", multiplex=1, async=0)


# make a blank list
l=[]

# iterate over all lysine's alpha carbons
cmd.iterate_state(1, "n. CA and resn lys", "l.append((x,y,z))")

# set a counter to 0 for controlling unique names
p=0

# iterate over all coordinates and create a
# pseudoatom at each lysine's alpha carbon
for ca in l:
    p+=1
    cmd.pseudoatom("pseudo%s" % (p), pos=ca, vdw=5.0)

# measure the pairwise distances across all pseudoatoms just created
cmd.distance("/pseudo*", "/pseudo*")



Many thanks,
James